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- PDB-7rel: Crystal structure of the first bromodomain (BD1) of human BRD4 in... -

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Basic information

Entry
Database: PDB / ID: 7rel
TitleCrystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor MA9-060
ComponentsBromodomain-containing protein 4
KeywordsGENE REGULATION / BET / JAK2 / dual BRD-kinase inhibitor
Function / homologyAmanitin/phalloidin toxin / toxin activity / Chem-4OW / Alpha-amanitin proprotein 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKarim, M.R. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Leukemia & Lymphoma Society United States
CitationJournal: To Be Published
Title: Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor MA9-060
Authors: Karim, M.R. / Schonbrunn, E.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7233
Polymers15,0991
Non-polymers6232
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 44.159, 78.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: Bromo 1 domain residues 44-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-4OW / N-[2-chloro-5-({2-[3-fluoro-4-(1-methylpiperidin-4-yl)anilino]-5-methylpyrimidin-4-yl}amino)phenyl]-2-methylpropane-2-sulfonamide


Mass: 561.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H34ClFN6O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulphate, 0.15 M Sodium chloride, 0.1 M Tris (pH 8.5), 25 % w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. obs: 19490 / % possible obs: 97.2 % / Redundancy: 4 % / Biso Wilson estimate: 12.94 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.036 / Rrim(I) all: 0.082 / Χ2: 3.26 / Net I/σ(I): 17 / Num. measured all: 77097
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.582.60.2388940.8980.1640.290.53988.8
1.58-1.612.70.2168680.9390.1460.2620.54791.3
1.61-1.642.70.1989340.9460.1340.240.57592.9
1.64-1.672.80.1888980.9510.1260.2280.58292.8
1.67-1.712.80.1589340.9590.1060.1910.69295
1.71-1.752.90.1539390.9620.1020.1850.69696
1.75-1.792.90.1329740.9770.0890.160.75398.8
1.79-1.8430.1159570.980.0780.140.72197
1.84-1.893.10.1049950.9820.0690.1260.912100
1.89-1.953.10.0879690.9870.0570.1040.89699.2
1.95-2.023.40.119910.9780.0660.1293.50999.5
2.02-2.13.90.1249980.9730.0690.1435.34398.9
2.1-2.240.1099800.980.060.1255.43499.1
2.2-2.324.30.1069780.9760.0570.125.28598.4
2.32-2.464.50.1029860.9860.0520.1155.17897.7
2.46-2.654.90.10110020.9880.0490.1125.03999.2
2.65-2.925.70.09810190.990.0440.1085.267100
2.92-3.346.40.08310040.9930.0350.094.47100
3.34-4.216.30.05610600.9960.0240.0613.371100
4.21-1005.90.04211100.9980.0180.0462.33599.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXF

3mxf


Resolution: 1.55→39.44 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 973 5 %
Rwork0.1628 18476 -
obs0.1643 19449 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.45 Å2 / Biso mean: 17.4027 Å2 / Biso min: 6.32 Å2
Refinement stepCycle: final / Resolution: 1.55→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 42 183 1287
Biso mean--15.58 27.3 -
Num. residues----127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.630.24841280.22422255091
1.63-1.730.21551310.16912506263794
1.73-1.870.21511390.18112622276198
1.87-2.060.19611400.159926762816100
2.06-2.350.19211410.15862674281599
2.35-2.960.18551430.16462716285999
2.96-39.440.17211510.153628603011100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.22450.09320.09050.25250.24490.21570.2121-0.2161-0.11470.0045-0.1687-0.13830.1191-0.0906-0.00550.20540.0378-0.01610.14160.02780.13414.637-9.246615.0618
20.26820.1177-0.22580.15060.01050.2366-0.0279-0.0486-0.04270.3579-0.056-0.0166-0.3381-0.1569-0.00770.2047-0.0011-0.02120.10550.00130.10799.931611.293420.7904
30.0239-0.00310.00580.02680.00720.03660.0151-0.0951-0.07660.0719-0.06770.0172-0.1841-0.2444-0.00160.10570.0298-0.00040.11030.00630.11184.24638.9086.9817
40.0742-0.0174-0.01430.03240.04280.0604-0.02660.139-0.0130.0148-0.04660.0271-0.0759-0.0545-0.02150.06350.0048-0.00370.1001-0.01480.08235.01682.0422-0.6833
50.13350.13280.09460.15750.01320.2389-0.01390.1358-0.08220.07650.0280.09940.0988-0.06370.06020.08810.01410.00680.079-0.00940.113912.4931-11.48673.383
60.0114-0.00430.01770.06580.05130.03510.0006-0.06130.10740.2005-0.0254-0.1040.03920.1636-0.00150.0780.0431-0.01160.12110.01890.086719.7874-6.34147.5584
70.04520.0109-0.01180.0871-0.04010.141-0.0438-0.09890.10250.1322-0.07450.1411-0.1129-0.1502-0.00890.1340.0039-0.00240.1054-0.01170.07139.99075.0817.7028
80.1441-0.1172-0.02310.1878-0.15550.236-0.00730.01660.03680.0632-0.0075-0.1821-0.05760.0132-0.02710.077-0.0067-0.01550.08510.00810.094218.09324.53616.7831
90.51060.2343-0.04440.1459-0.08450.1063-0.0560.2426-0.0394-0.30530.205-0.0593-0.12740.19940.15490.1533-0.02290.06730.1685-0.00530.093819.0407-2.3584-8.1983
100.1351-0.04930.06020.2199-0.21990.1984-0.09180.11950.0716-0.20610.13710.0522-0.05680.0267-0.00090.0828-0.0078-0.00160.08880.01510.104512.127510.0231-0.7046
110.02690.01530.00390.02740.02540.0260.0192-0.3217-0.08090.3160.0385-0.1237-0.2473-0.01430.00020.370.0056-0.0170.1891-0.02470.218311.651922.559616.8371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 51 )A42 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 68 )A52 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 75 )A69 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 83 )A76 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 96 )A84 - 96
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 106 )A97 - 106
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 121 )A107 - 121
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 139 )A122 - 139
9X-RAY DIFFRACTION9chain 'A' and (resid 140 through 144 )A140 - 144
10X-RAY DIFFRACTION10chain 'A' and (resid 145 through 163 )A145 - 163
11X-RAY DIFFRACTION11chain 'A' and (resid 164 through 168 )A164 - 168

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